Potential pitfall when the subset indices is a Rle vector of TRUE and FALSE

[andyyhchen]

https://github.com/GreenleafLab/ArchR/blob/c61b0645d1482f80dcc24e25fbd915128c1b2500/R/AllClasses.R#L723

The Rle vector will not go in any of the if condition and will be send to the unique(). This will make the Rle list become a two element list of TRUE and FALSE. Adding i <- as.vector(i) before if (is.logical(i)) will fix this.

Here is the code on how to reproduce this bug. proj[proj@cellColData$Sample == 'Sample1',] and this will end up subseting half of the proj cuz the broadcasting of c(TRUE, FALSE).

But user should be safe if they always access cellColData using $ sign since the dollar sign operator function does as.vector(x) before returning the values. https://github.com/GreenleafLab/ArchR/blob/c61b0645d1482f80dcc24e25fbd915128c1b2500/R/AllClasses.R#L679

Hence proj[proj$Sample == 'Sample1',] will output the correct subset.

[rcorces]

Hi @andyyhchen! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.
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[rcorces]

thanks for posting. This has been updated in the dev branch. Worth noting that we no longer recommend subsetting projects like this and encourage users to use subsetArchRProject() which is more stable